I've encountered a very interesting situation. I believe that almost everyone suffered non-lethal ammo rack damage during their WoT-lifetime.
I wondered that if someone manages to damage your ammo rack, the reload time significantly increases (about 2x), despite the location of your ammo rack's damage.
(Also, if your ammo rack gets damage, your crew says that "We lost some ammo, but at least it didn't explode")
For example at the ARL 44 there are at least three places inside the tank where the crew stores the ammunition, and wherever it gets shot, the increase in reload time will be equal every time.
If your ammo rack gets hit while it still contains ammunition, the ammunition in the damaged rack would be unable to use (not all, it should be depend on the quantity of ammos in the rack).

My suggestion would be the following:
If your ammo rack gets damaged, you'd lose from the ammunition inside that (depends on the seriousness of the damage), and you'd get a significant increase in reload time for a limited time (while your loader checks the intact ammunition, maybe sorts it), after that the reload time will remain the original.